Fig. 1

Schematic diagram of the RegionIndel pipeline. Input data are the high-quality reference genome and barcoded reads, each with a barcode (not shown). The reads extraction module extracts barcoded reads aligning to the region of interest. The reads with the same barcode (read cloud) form the virtual long fragment molecule. The haplotyping module partitions molecules into different parental haplotypes, and then the corresponding barcoded reads will be partitioned into different haplotypes. The local assembly module takes barcoded reads and performs de novo local assembly independently for each haplotype through SPAdes. Finally, the variant calling module integrates paftools to perform a contig-to-reference comparison to detect all variants